The Last and the Only: Leftover Angel
by Vilinye
Summary: After Sarah Jane's death, Luke Smith joins the 11th Doctor in the TARDIS. Their first stop looks familiar-but something sinister is going on. Loose sequel to the updated My Sarah Jane, and the first of six in a new series.
1. Prolouge

She runs. Runs for her life. The signal won't be off long, but she has to get away before he notices. Maybe she can hide for a day, an hour, a minute—get away from their control before another test comes.

Behind her, the dull thud of a Sontaran trooper sounds on the pavement. Just one, but one could still ruin everything… She flaps one wing, but the other, dangling loosely on her right side, drags in the dirt.

A sign dangles overhead, scribbled with words she cannot read. She shuffles through the door, trying to keep watch for anyone coming. Without watching her steps, it is too late to stop herself from tumbling down the stairs. When the tumbling stops, she sinks to the ground, curling up as small as she can. Her lips move, but no air is left for words. …


	2. Chapter One

"Right then, see you later. Have fun snogging," He made a face that reminded Amy of apples in the kitchen.

Amy kissed the Doctor's cheek. "Keep in touch, okay?"

"Of course. Just a quick trip around the galaxy."

"Come on, Mrs. Williams. I'm sure your parents will want an explanation for everything," Rory rolled his eyes and pointed up to a lit bedroom window.

"That's Mrs. Pond to you. " Amy retorted. "Besides, the Doctor said it's just two weeks after we left. I'm sure they came to their own conclusions."

"I don't mean just about this. I mean—" Rory pointed to the blue box. "This."

"They can just mind their own business." Amy's expression suggested they'd be foolish to do anything else.

"Right, then. See you around, Ponds."

"You sure they don't mind leaving?" Luke asked. "I don't want you to kick them out for me."

The Doctor shut the TARDIS door. "Nonsense. They got tired of my honeymoon suggestions after the carnivorous planet. Didn't even bother coming out on Alres."

"Alres was fascinating. Those people glowed."

"A result of firefly DNA inserted into their genome several centuries ago. The local torch manufacturers were none too pleased."

"So… where to now?"

"Wherever you like. Maybe I'll even let you fly the TARDIS. As long as you don't start thinking you know better than me. And don't even think about trying to fix the chameleon circuit."

"I won't," Luke smiled.

"Right then. Let's start with the wibbley lever!"

"How strange," The Doctor poked his head out the door and looked around. "It looks like a normal Earth town. Orbits a binary star, so it has two suns, but as long as you don't look up, it could be a London 'burb."

"Why is that strange?" Luke asked.

"Because, most of the time, towns have _people_; it's kind of in the definition of a town. But no one's here. Look around, no mothers shopping, no businessmen hustling around, no teens out for fish and chips." The Doctor extended his sonic and glanced at the readings. "What's wrong with you, hm? It says four biological life forms in immediate area." He pointed at a door half a block down, where a brunette holding a baby stared blankly at a Sontaran trooper. "Then why do I count five?"

The Sontaran pointed his gun barrel at the woman. "Stand aside, or suffer the wrath of the glorious Sontaran Emperor. "

"Shouldn't we do something?" Luke asked.

"Shh." The Doctor adjusted a setting on his screwdriver. "I'm getting very interesting signals here, and—ah!"

The Sontaran fired. But instead of screams and gasps, the woman and her child disappeared. No blood fell to the ground; no corpses filled the doorway. The Sontaran kicked the empty air. "Well, for training, that was fine, but I'm ready for action."

"Training?" Luke sputtered.

"He's turning this way. Get down."

Luke and the Doctor dropped to the ground. After a brief survey, the soldier pressed a button on his wrist and disappeared. Slowly counting to one hundred, Luke finally stood up. "Well, what do you think of that?"

"From what I can tell, the woman and the child were holograms. The Sontaran, on the other hand, was real. He must have access to some sort of teleport device. That's not good, not good at all."

"I've faced Sontarans before." Luke pointed out.

"Yes, but we need to discover what exactly this place is first. There's something wrong about it, and I want to learn what it is. Now my sonic says we have three life-forms in this area, and the third is unidentifiable. "

"Can you figure out where it is?"

"Well, let's go poke things with a stick—see what comes out."

The Doctor paused outside a pub. "The readings say it's in there. Let's go take a look, Luke. Oh, look-Luke, that sounds cool. Looky-lukey, look luke luck."

Luke grinned. "Mum always said you were a little bit off, but this version is even crazier than most."

"Oye, listen. Eyes on the tie, and listen up. It's cool, I'm the man with the plan," The Doctor adjusted his bow tie. "Come on, let's go inside."

The dank, crowded room had tables and chairs, but was surprising clean. No posters, no dirty napkins, no gum under the table. "Well, no one's here. Wait…let's check the cellar. Here's the stairs—watch your head, it's very low. Smells down here, but that's to be expected, even with no people, basements always smell a little musty and gross." The Doctor turned on his screwdriver light. "Hello, it's the Doctor, anyone here? Someone's definitely here."

Luke followed him, peering into the shadows. "We don't want to hurt you; we just want to find out what's going on here."

"Did you hear that?" The Doctor lowered his voice. "I hear breathing." He took a step forward, holding the sonic like a torch. "I don't want to hurt you. Unless you want to hurt me or my friend. In which case I definitely will hurt you."

"If anybody wanted to hurt us, they would have done it by now." Luke pointed out. " Which means you're probably scaring somebody who's harmless."

" Mmm…good point. Why don't you try, Luke?"

"Me?"

"You have experience talking with friendly aliens. Maybe you could introduce me to some of them later—the ones I meet all tend to want to kill me."

"Right," Luke grinned. He got down on his hands and knees. "Listen, we know you're there, but we aren't going to hurt you. Are you okay? "

A soft whimper came from the darkness.

"Can you say something? Do you need help? My name is Luke, and this is my friend the Doctor."

Something moved towards the light. At first, all they could see were two blinking eyes, huge as plums. The face was basically human, with dark eyes set above a bony nose and a bald head. Two leather sheets hung at its side, emphasizing the painful thinness. Below the sheets, Luke saw that the toes were long and thin like fingers, with three joints.

"Help. Help me," it wheezed.

"We will. " Luke promised.

The Doctor took the screwdriver and pointed it at the figure's arm.

"No, no…don't hurt me, don't hurt me." The words came out in a frantic babble. "I did the mission, I did the mission."

"Mission?"

"He's not going to hurt you. He's just trying to find out how to help you. The metal thing is is sonic screwdriver, and it's not a weapon."

"Really?"

"Really." Luke nodded. "Trust me, okay?"

The Doctor stepped closer, and this time the child didn't flinch. "Shh, I want to help. Where are we? What is this place?"

"The training ring. Owner has armies practice fighting here. They practice, then go everywhere. Sontarans, Judoon, Draconian …"

"Really?" The Doctor tilted his head. "That's definitely something I ought to investigate. But for now, let's see what I can find out. Female, definitely. The DNA is almost readable, but with extra bits that throw off the settings."

"What sort of extra bits?" Luke craned his neck to read the results.

"Enlarged cardiac vessel, altered metabolism, air sacs instead of alveoli, oviparous, infrared vision, prehensile feet…" The Doctor looked up. "Haven't encountered aliens like this before. Which means—" He stared at Luke. "She's not alien."

"Well, what is she, then?" Luke asked.

"Genetic code is mostly human, but the extra bits mean someone's been tampering with her genetic structure, and that means we have more going on here that just some Sontarans learning to fire guns. That requires enormous amounts of knowledge, skill, and money."

She coughed again. "What's wrong with me?"

"I'm not sure." The Doctor looked in her eyes. "I would need more information to help you. And for that, I have to find the person who runs this place. "

"Owner only wants to see customers. "

"Customers for what?"

"Me."

"You." The Doctor repeated.

"Me. He wants to sell me. There have been a few offers, but the price wasn't high enough."

"Well then, can you direct me to this 'Owner?'" The Doctor's eyes darkened. "I definitely have some business with him. "


	3. Chapter Two

"Dorium, I didn't expect you; I mean, what brings you here?" Despite the air-conditioned office, the speaker's pale skin glistened with globs of sweat.

"You know why I'm here," Dorium stared at the asteroid's owner, a short, balding humanoid with silver eyes. "I heard rumors that you have been seeking other buyers for the project."

"Really?" he babbled. "You must have been misinformed. I was just investigating the going rate for genetically engineered soldiers."

"A likely story, Scen. You were planning to clone it and sell the copies at an astronomical price." Dorium glanced around the office, full of uncovered pipes and wiring. "Certainly you could use the money."

"No, no, I swear."

"Pity," Dorium produced a pipe from his robe. "That's what I would have done."

"Would you like to see the final product? I'm sure the Church would appreciate an eyewitness account of the results,"

"Of course," Dorium lit his pipe. "So, where is it?"

"I was running it through the simulation against a Sontaran—live practice, you see, and well… the signal was disrupted."

"You lost it?"

Scen shrank back, pressing himself against a steel beam. "I know exactly where it is. But there's two more life signs in the arena now."

"Bring the unit here, and then worry about them, hm?"

"Of course, certainly, right away," He flipped a few switches on the wall. "The visual feed should come through easily enough, but the audio feed—"

"Stop babbling."

The wall pixelated into a jostled close-up of a tweed jacket, with words filtering in moments later. "Luke, can you open that door?"

* * *

><p>"Luke, can you open that door?" Since the girl was roughly a meter, the Doctor could carry her on his shoulder.<p>

"So, what's the plan?"

"Plan? Do I have to have a plane? I've barely started talking."

She leaned her head against his shoulder. "I don't want to—no, don't make me." The leather canopies flapped wildly, slapping his shoulder. "Sorry—sorry—" But even before she finished apologizing, her legs shot out, kicking him in the gut.

"Offf," The Doctor grunted, accidentally dropping her, as he doubled over in pain. "Why the kick?"

"Sorry, sorry."

"That would be more of a constellation if you didn't keep hurting me." He straightened up, adjusting his bowties.

"Not me. Owner did it." She stumbled to her feet. "You see—owh. OWH. " The canopies shuddered again, extending over two meters on each side. They beat down, once, twice, with one dangling at a rough angle as her body slowly lifted from the ground. "Don't want. Don't want this," she cried, as each downbeat carried her further away.

"Doctor, what's going on?" Luke stared at the slowly shrinking silhouette on the cloudless, almost marker-streaked, sky. The flight path, erratic and jerky under the dual suns, just reminded him of how far from home he was.

"Well, judging from the data I have, and under the circumstances, I suspect that something is wrong here. Very wrong. I suggest we track her to this mystery owner. Wish you'd brought K9, he could have isolated a trace of her DNA."

"You mentioned genetic manipulation—what type? I've been reading up on Mr. Smith's files, and there's several different methods. For example, what Mrs. Wormwood did with me as the archetype involved scanning a huge population and combining the results to create one 'perfect' being. On the other hand, clone races like the Sontarans have an assembly-line method. Also, there's the-"

"I haven't had time to run a complete analysis, especially without the TARDIS's equipment, but based on the modifications I discovered; it's likely she was the product of handwork. Not actual handwork of course, probably lots of robots and nanogenes and tiny things like that, but most likely an original design. Kind of like Michelangelo's _David _versus a paint-by-number, except made of living cells and bone and DNA and wings and prehensile feet—you know what, forget that, it's nothing like that." The Doctor looked at the sonic. "She's not moving very fast, but that means we can track her down more easily. Come on, who wants to go for a run?"

* * *

><p>"That's your idea of retrieving the project?" Dorian blew out a puff of smoke. "If they didn't suspect anything from its words before, they certainly will now. And you couldn't even manage a decent visual on the intruders."<p>

Sweat beaded Shen's brow. "You don't understand how fragile the human brain is. Too much force could leave her a vegetable, incapable of the analyzing power the Monks requested. The trainer was working on a less invasive method, but after the electrodes backfired—"

"I have heard nothing of this."

"The trainer suggested implanting neuron communicators in both their brains for direct communication with the project at all times. But the controllers accidentally relayed the message to the trainer's brain as well, causing severe brain damage. "

Dorium set down his pipe. "To the project?"

"To the trainer. She barely survived. The project had to be sedated—I suspect the pain was also relayed via the neuron circuits." Shen finally met Dorium's eyes. "You may be on commission with the Headless Monks, but you don't understand the intricacies of genetic engineering. And if you wish to return and explain that their latest investment now has the mental state of an Adipose because you tried to manage the controls, I would love to see their reaction."

Two pairs of eyes stared into each other, trying to gage the situation. Finally, Dorium leaned back. "So, we understand each other."

"Quite well, I suspect." Shen turned to the screen. "It seems the homing activator was successful. Here comes the little bird now." He pressed a button, and a two-meter cube slid out of the wall, white sides fading to clear.

The girl crouched inside, wings pressed against her shaking body. "No. No."

"You ran away." Shen didn't bother glancing at her.

"Can it understand you?"

"That was the order, wasn't it? Wouldn't do much good to have the ultimate weapon if she couldn't communicate. Hasn't said much since the trainer died. Seems to have regressed. But I can generally shock it into communicating. Whom did you met?"

Her eyes flicked to Dorium, then back to a corner of the room.

"Whom did you meet?" Shen repeated.

"Who that?"

"I'll ask the questions," Dorium strode over to the wall, standing right against the cage. "Who was that?"

Her injured wing shuddered involuntarily, striking the interior glass. She tried to back away, but the floor was too slick and the cage too small.

"I know you can understand me. Who else was in the arena?"

"Judoon,"

"Is she really that stupid?" Shen scoffed. "Or is she actually trying to lie to us? Either way—" he pressed another button on the control panel. "Just a jolt to the pain centers."

She shuddered for a moment, then recovered.

"Who else was there?" Dorium repeated.

"Man. Boy."

"Any names?"

"Boy is Luke."

"And the other one?"

"Talked a lot. Wore something around his neck. Big words. Metal round thing, made noise—_eeee._" Her round eyes stared into the distance. "Said he had business with you."

"A potential customer?" Dorium glanced back at Shen. "Maybe you should bring him in now too. The arena is equipped with an underlying transmit system, correct?"

"How did you know that—don't answer," Shen corrected himself. "I run an honest business here, I'm not interested in your tricks."

"Honest?" Dorium took another breath from the pipe. "You may continue deceiving yourself, if that is what you wish to do. But spare me your babble. Bring this man here to speak for himself."

"Of course."

"And then we shall test the project's skill in mortal combat. After all, you wouldn't want the Monks finding out what you were planning, would you?"

Shen swallowed at the implied threat. "Certainly not." He pressed in the activation code for the transmit, quickly isolated the oldest of the life forms, keyed in the destination coordinates, and waited for the new arrival.


	4. Chapter Three

Air swirled in a six-foot column, slowly revealing a floppy-haired, wild-eyed young man in a tweed jacket and blue bow tie. "Remote teleportation device. Good, very good. "

"How did you find us?"

"Oh, you know, just followed the big bird person. Look, you left some of my friends behind, can you just zap them here?"

"We understand that you expressed interest in the project," Shen continued.

"Interest? Well, I suppose that is one word you could use, some others come to mind: concern, care, wonder, caution, but yes, interest will do." The Doctor waved his hands toward the cage. "Where did you come from? What are you doing with her?"

"First of all, I must have your solemn promise that you will keep this keep this information in strictest confidence. Can't have rumors getting out, Mr-?"

"Smith."

"Mr. Smith? Of course, if you want to maintain your privacy we respect that right." Dorium replied smoothly. "So, do we understand each other?"

"Maybe. I think we should talk some first. Talking is good."

Shen and Dorium exchanged glances. "Is there anything specific you want to know about?"

"Just spill the beans, dish out the gravy, mash the potatoes—is that the right? Tell me everything."

Shen cleared his throat. "We began with inserting chiropteran DNA in the zygote stage. During further development, we inserted electrodes in the brain tissues to enable electronic control of the limbs, as well as electronic camera lenses in the eyes. Further stimulation sparked low-lever telepathic abilities. "

"Electrodes in the brain?"

"It's like an old remote-controlled car, but alive. Instead of unmanageable metal , though, we have living flesh." Dorium coughed. "Is that a satisfactory answer, Mr. Smith?"

"But why, what for?"

"A weapon. The DNA is still pure enough to pass for human, enabling it to slip past enemy lines unnoticed, but the training makes her far more deadly than a bomb. She can wield any weapon, carry twice her body weight for a quarter of an hour, and live for a week on minimum rations."

"And whose idea was this?" The Doctor stared at them.

Dorium shook his head slightly. "I'm not at liberty to say."

"Really?" The Doctor pulled out his sonic and stared down at it. "Because I have some words for them."

"Mr. Smith, would you like to see a demonstration of the project's skills?" Shen's fingers hovered over the rows of buttons.

"No thank you, I'd rather not."

"Pity." Dorium nodded to Shen. "Because you were going to be the opponent."

* * *

><p>"…The chromosomes bear resemblance to axillary membranes, especially at the k-32 substring, which leads me to believe—" The air around the Doctor rippled like a summer mirage. His words were cut off for a moment, then he disappeared.<p>

"Doctor?" Luke stared. "Great. No scanner watch, no sonic, no robot dog, and I'm stuck in an alien training compound. "Well, I'm not just waiting for him to come back. Aliens that kidnap people generally aren't friendly. Might as well keep heading in this direction."

* * *

><p>The glass cage slide open. The girl remained huddled in the back, but another button shocked her into action. She lunged forward, nearly falling but regaining her balance.<p>

Dorium stepped into a corner; Sheen remained at the control panel.

Unable to fly, she leapt onto a cabinet in the corner. From there, she sprang onto the Doctor's shoulder, her talons digging into his skin.

He waved his arms wildly. "Shoo! Get off me."

She slid off, landing on his foot. "Sorry."

"Stop apologizing, fight!" Shen snapped, pressing another button.

The Doctor stepped back as the girl punched. She swung again, missing.

"I know you can do better than that!" Shen flicked a switch.

She jumped onto a box, then dove onto the Doctor's neck.

"Buttons, yes," The Doctor mused as her claws squeezed his throat. "Not quite sporting, is it?" Ignoring the girl perched around his back, he reached into his jacket and pulled out the sonic. "Ah!" He pointed it at the control panel.

A spark fizzled below Shen's thumb. "Is that all you can do, Smith?"

The Doctor shrugged.

The girl fell to the floor, eyes closed.

"That's better. Now let's talk."


	5. Chapter Four

The Doctor scanned the girl's body. "She'll be fine, as soon as I get her away from you lot."

"Are you prepared to make an offer then?" Shen's eyes reflected the light like a dead fish's. Ignoring the glance Dorium shot at him, he took a step forward. "So, to whom shall we send the bill then, Smith?"

"My name isn't Smith."

"Well, then are you ready to drop this pretense and tell me who you really are?"

"You don't want to know."

"Oh, I think I do." Dorium interjected.

"Don't toy with me. I know what you're thinking: _oh, he's just a silly young man with a bowtie, what can he do to us?_ You think this is none of my business, but when you sell people like fish and chips, when you try to make the perfect soldier, when you create a child as a weapon—"His voice dropped into icy calm. "Then it becomes my business."

"Again, what is your business?"

The Doctor pulled out his sonic and tossed it into the air. "I could destroy your circuit board with a few pulses. Just answer a few questions. Who requested this?"

"The Church."

'Doesn't clarify things much. What church?"

"Modern. 51st century." Shen gulped.

"And they wanted a weapon?"

"Yes. They wish silence to fall. By destroying the mighty warrior, they hope to bring about their goal."

"And this is the result of their grand scheme? One terrified child?" The Doctor gestured to the huddled lump on the floor.

"I had a rudimentary knowledge of genetic engineering from previous projects—the training arena is just a cover story," Shen babbled. "The process was so complicated, you would not believe how many failures I suffered, how many times I contemplated giving up, but I persevered. And she is just the beginning."

"I knew someone like you once…an egomaniac determined to create his own race of beings, war machines without a single weakness."

"It wasn't my idea! I work on commission!"

"He died at their hands. More than once, actually, but that's a long story. And his race spread terror and destruction among the stars. That is not going to happen again."

"You want to kill it?" Shen fumbled for a pistol. "I can do that."

"Guns! What is it with the guns?" The Doctor snatched it away and kicked it into a far corner. "No, I do not want you to kill it. And it's not an _it_. Doesn't she have a name?"

Shen shrugged. "The trainer might have given it one."

"And this trainer?"

"Dead."

* * *

><p>A concrete bunker rose out of the empty streets. Luke circled it from a distance. "No doors—just a square opening a meter high. "<p>

He stepped up to the wall. "Well, I hope he's in here. Here goes nothing."

"…and if you would just let me find my friends, I would go on my way."

"No need." Luke announced, his head sticking out of the glass cage on the far wall. "Hello, Doctor. I don't suppose you've found a door."

"Luke! How did you find me? "

"Just kept heading in this direction—oh, this is a tight squeeze. What is it, an air vent or something?"

"No, that's how the project gets in." Shen interrupted.

"So, not an air vent. But your mum had experience with air vents. Can you get your hands out of the shaft?"

"I think so…there!" Luke winced. "Could you give me a hand?"

"Of course—excuse me a moment, gentlemen. " The Doctor grabbed Luke's hands and pulled, letting him tumble into an upright position. "So, now that we have that problem sorted, I'll just be off." He knelt by the girl. "Hey, are you okay?"

"I'm sorry," she whispered.

"Don't worry now. I'll take care of that."

"Um, Doctor," Luke began. "I don't think the blue guy likes that idea much."

"He doesn't have to like it."' The Doctor bent over the girl. "This is going to hurt. But trust me. I'm the Doctor."

She stared up at him, eyes wide. Finally she nodded.

The Doctor flipped a few settings on the sonic and inserted one end in her left ear.

Her eyes rolled up in her skull. Her fists clenched and her tongue lolled out of her mouth. For a moment, Luke thought she was dead. Then she went limp.

"She'll be fine. I just disabled the electrodes in her brain. Luke, the teleport's in the corner, I'll give you the teleport coordinates to send us back to the TARDIS."

"You think you're just going to walk off?" Dorium protested.

"Well, I could have linked those electrodes to your brain, or stuffed you in a cage, or even killed you, but I don't really want to do that. So I'll just leave you to the mercies of your employers. " The Doctor picked up the sleeping girl. "Luke, I see you've got K9. Good, let's go."

"Who do you think you are?" Shen stepped up to him.

"Me? I said call me Smith, but most people call me the Doctor."

As the Doctor stepped onto the transmit platform, he noticed Dorium's skin turning robin's egg blue.

* * *

><p>"Well, this is the TARDIS. What do you think of it?" The Doctor spread out his arms.<p>

She was awake now, staring around the glass room. "Bigger on the inside."

He winked. "Yes, you'll get used to it. Now, first things first. Do you have a name? Preferably something short enough that I can shout it when you decide to wander off?"

"My trainer used to call me Gwen."

"That's a pretty name. " Luke took her wing in his hand. "Come on, let me show you around. You won't believe what's in here."

* * *

><p><strong>NEXT TIME in The Last and the Only:<strong>

Gwen pressed her hands against the clear surface, trying to break free. "I can't !" she called, but her words could not penetrate the prison. Down below, she could see another module closing in around Luke and the Doctor. Above their heads, halfway down their bodies—then arcs of blue energy and the Doctor was gone.

**A Prison of Air**


End file.
